Introduction
Luciferase is the alpha-beta heterodimer monooxygenase enzyme responsible for catalyzing the light producing oxidation reaction in luminescent bacteria.  Its official name is alkanal monooxygenase (EC 1.14.14.3), but I'm sure that it would prefer being called luciferase since that makes it sound like one tough enzyme.  The substrate that a luciferase acts on is generally called luciferin (for more information on this general interaction, feel free to jump on over to the bioluminescence section of this site); in the specific case of bacterial luciferase, the specific substrates which the enzyme acts upon are reduced riboflavin 5'-phosphate (FMNH2), long-chain aliphatic aldehyde (R-CHO), and of course, molecular oxygen.  The products of the reaction are FMN, H2O, and visible blue-green light (490 nm).  Bacterial luciferase is a unique flavoprotein in that it utilizes reduced flavin molecules as substrates instead of using them as tightly bound co-factors.  The reaction scheme is shown below, with an accompanying description of the reaction steps involved.
 

 
Luciferase Reaction Scheme
 
Figure adapted from Biochemistry (4)
 
The first step of the reaction is the activation of luciferase-bound N (1)-deprotonated FMNH- by O2 to form the FMN-4a-hydroperoxide intermediate (II).  Subsequently, the aliphatic aldehyde reacts with intermediate II, resulting in the formation of the FMN-4a-peroxyhemiacetal intermediate (III).  Both an alkylhydroxyoxy radical and a FMN-4a-hydroxide intermediate (IV.) radical are then formed due to the intermolecular electron transfer within intermediate III.  The alkylhydroxyoxy radical then undergoes a transformation into a carbon-centered alkylhydroxy radical and donates its extra electron to intermediate (IV.).  As a result, RCOOH as well as FMN-4a-hydroxide (IV*), which has been induced into an excited state, are formed.  The excited state intermediate eventually decays and produces light and brings it to its ground state (IV); finally, via dehydration, the ground state IV molecule yields FMN and H2O.  An alternate path exists in which intermediate II, rather than reacting with the aldehyde, undergoes a dark decay to produce FMN and H2O2 without the release of light energy. (5)
 

 
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